Skip to content

Commit 29768e5

Browse files
jiywang3jiywang3
committed
Pull request #654: Switch electron density data from RCSB DSN6 to PDBe Density Server.
Merge in STRUC/icn3d from release3333 to master * commit 'fbd88daadb6ccd10603f8ec55259e9bb4ffe8dd1': Switch electron density data from RCSB DSN6 to PDBe Density Server.
2 parents c8f233d + fbd88da commit 29768e5

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

41 files changed

+805
-248
lines changed

‎CHANGELOG.md

100644100755
Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,7 @@
11
## Change Log
2-
[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle".
2+
[icn3d-3.33.3](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.3.zip) was release on July 15, 2024. Switch electron density data from RCSB DSN6 to PDBe Density Server.
3+
4+
[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.2.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle".
35

46
[icn3d-3.33.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 18, 2024. Draw coils for the whole structure with zero radius for the secondary structure parts.
57

‎LICENSE.md

100644100755
File mode changed.

‎README.md

100644100755
File mode changed.

‎SECURITY.md

100644100755
File mode changed.

‎build/icn3d.js

Lines changed: 152 additions & 43 deletions
Large diffs are not rendered by default.

‎build/icn3d.min.js

Lines changed: 3 additions & 3 deletions
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

‎build/icn3d.module.js

Lines changed: 152 additions & 43 deletions
Large diffs are not rendered by default.

‎dist/CHANGELOG.md

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,7 @@
11
## Change Log
2-
[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle".
2+
[icn3d-3.33.3](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.3.zip) was release on July 15, 2024. Switch electron density data from RCSB DSN6 to PDBe Density Server.
3+
4+
[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.2.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle".
35

46
[icn3d-3.33.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 18, 2024. Draw coils for the whole structure with zero radius for the secondary structure parts.
57

‎dist/full.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,11 +19,11 @@
1919
<div id="div0"></div>
2020

2121
<link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
22-
<link rel="stylesheet" href="icn3d_3.33.2.css">
22+
<link rel="stylesheet" href="icn3d_3.33.3.css">
2323
<script src="lib/jquery-3.5.0.min.js"></script>
2424
<script src="lib/jquery-ui-1.13.2.min.js"></script>
2525
<script src="lib/three_0.151.0.min.js"></script>
26-
<script src="icn3d_3.33.2.min.js"></script>
26+
<script src="icn3d_3.33.3.min.js"></script>
2727

2828
<script type="text/javascript">
2929

@@ -41,7 +41,7 @@
4141
alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
4242
}
4343
else {
44-
//$.getScript('icn3d_3.33.2.min.js', function() {
44+
//$.getScript('icn3d_3.33.3.min.js', function() {
4545
var version = 3;
4646
await launchIcn3d(version); //await
4747
//});

‎dist/full2.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,11 +20,11 @@
2020
<div id="div1" style="float:left;"></div>
2121

2222
<link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
23-
<link rel="stylesheet" href="icn3d_3.33.2.css">
23+
<link rel="stylesheet" href="icn3d_3.33.3.css">
2424
<script src="lib/jquery-3.5.0.min.js"></script>
2525
<script src="lib/jquery-ui-1.13.2.min.js"></script>
2626
<script src="lib/three_0.151.0.min.js"></script>
27-
<script src="icn3d_3.33.2.min.js"></script>
27+
<script src="icn3d_3.33.3.min.js"></script>
2828

2929
<script type="text/javascript">
3030
$( document ).ready(async function() {
@@ -41,7 +41,7 @@
4141
alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
4242
}
4343
else {
44-
//$.getScript('icn3d_3.33.2.min.js', function() {
44+
//$.getScript('icn3d_3.33.3.min.js', function() {
4545
var version = 3;
4646
await launchIcn3d(version);
4747
//});

‎dist/full2_3.33.2.html renamed to ‎dist/full2_3.33.3.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,11 +20,11 @@
2020
<div id="div1" style="float:left;"></div>
2121

2222
<link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
23-
<link rel="stylesheet" href="icn3d_3.33.2.css">
23+
<link rel="stylesheet" href="icn3d_3.33.3.css">
2424
<script src="lib/jquery-3.5.0.min.js"></script>
2525
<script src="lib/jquery-ui-1.13.2.min.js"></script>
2626
<script src="lib/three_0.151.0.min.js"></script>
27-
<script src="icn3d_3.33.2.min.js"></script>
27+
<script src="icn3d_3.33.3.min.js"></script>
2828

2929
<script type="text/javascript">
3030
$( document ).ready(async function() {
@@ -41,7 +41,7 @@
4141
alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
4242
}
4343
else {
44-
//$.getScript('icn3d_3.33.2.min.js', function() {
44+
//$.getScript('icn3d_3.33.3.min.js', function() {
4545
var version = 3;
4646
await launchIcn3d(version);
4747
//});

‎dist/full_3.33.2.html renamed to ‎dist/full_3.33.3.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,11 +19,11 @@
1919
<div id="div0"></div>
2020

2121
<link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
22-
<link rel="stylesheet" href="icn3d_3.33.2.css">
22+
<link rel="stylesheet" href="icn3d_3.33.3.css">
2323
<script src="lib/jquery-3.5.0.min.js"></script>
2424
<script src="lib/jquery-ui-1.13.2.min.js"></script>
2525
<script src="lib/three_0.151.0.min.js"></script>
26-
<script src="icn3d_3.33.2.min.js"></script>
26+
<script src="icn3d_3.33.3.min.js"></script>
2727

2828
<script type="text/javascript">
2929

@@ -41,7 +41,7 @@
4141
alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
4242
}
4343
else {
44-
//$.getScript('icn3d_3.33.2.min.js', function() {
44+
//$.getScript('icn3d_3.33.3.min.js', function() {
4545
var version = 3;
4646
await launchIcn3d(version); //await
4747
//});

‎dist/icn3d-3.33.2.zip renamed to ‎dist/icn3d-3.33.3.zip

4.44 MB
Binary file not shown.

‎dist/icn3d.html

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -896,7 +896,11 @@ <h3>Frequently Asked Questions<img src="https://www.ncbi.nlm.nih.gov/Structure/I
896896
</li>
897897

898898
<li><span class="anchor" id="igrefnum"></span><a name="igrefnum"></a><b>Q: How to use iCn3D to assign Ig reference numbers?</b><br>
899-
You can assign IgStrand reference numbers via the menu "Analysis > Ref. Number > Show Ig for Selection", or via the menu "Analysis > Seq. & Annotations" and click the checkbox "Ig Domains" in the "Annotations" section. The reference numbers can be exported via the menu "File > Save File > Reference Numbers". See the manuscript <a href="https://www.biorxiv.org/content/10.1101/2024.06.10.598201v1">A universal residue numbering scheme for the Immunoglobulin-fold (Ig-fold) to study Ig-Proteomes and Ig-Interactomes</a> for more details.<br>
899+
iCn3D provides an automatic way to detect Ig domains and assign "IgStrand" reference numbers for all residues so that users can cross-compare residues in different Ig domains using the reference numbers.<br>
900+
<br>
901+
A list of about 55 Ig templates are used to align the input structure using TM-align. The template with the highest TM-score is selected as the template to assign the reference numbers for each strand in the Ig domain. Different from Kabat and IMGT reference numbers for Ig domains, "IgStrand" reference numbers are similar to GPCR reference numbers. An anchor residue in each strand is assigned a 4-digit number ##50. For example, the refernce number 1550 is the anchor residue for "A" strand. The residues before and after the anchor residue are assigned as continuous numbers: ##48, ##49, and ##51, ##52, respectively. Each strand has a predefined color so that users can easily tell the strands from the color. See the manuscript <a href="https://www.biorxiv.org/content/10.1101/2024.06.10.598201v1">A universal residue numbering scheme for the Immunoglobulin-fold (Ig-fold) to study Ig-Proteomes and Ig-Interactomes</a> for more details.<br>
902+
<br>
903+
You can assign IgStrand reference numbers via the menu "Analysis > Ref. Number > Show Ig for Selection", or via the menu "Analysis > Seq. & Annotations" and click the checkbox "Ig Domains" in the "Annotations" section. The reference numbers can be exported via the menu "File > Save File > Reference Numbers".<br>
900904
<br>
901905
If you want to process a list of structures, you can download iCn3D Node.js script "refnum.js" at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This script runs TM-align locally using the program at https://github.com/ncbi/icn3d/tree/master/icn3dnode/tmalign-icn3dnode and the templates at https://github.com/ncbi/icn3d/tree/master/icn3dnode/refpdb. One example is listed at the section “Detect Ig domains and assign IgStrand reference numbers” at https://github.com/ncbi/icn3d/tree/master/icn3dnode.<br>
902906
<br>

0 commit comments

Comments
 (0)